Bioconductor - factR

Bioconductor - factR
Bioconductor 3.22
Software Packages
factR
factR
This is the
released
version of factR; for the devel version, see
factR
Functional Annotation of Custom Transcriptomes
DOI:
10.18129/B9.bioc.factR
Bioconductor version:
Release (3.22)
factR contain tools to process and interact with custom-assembled transcriptomes (GTF). At its core, factR constructs CDS information on custom transcripts and subsequently predicts its functional output. In addition, factR has tools capable of plotting transcripts, correcting chromosome and gene information and shortlisting new transcripts.
Author:
Fursham Hamid [aut, cre]
Maintainer:
Fursham Hamid
Citation (from within R, enter
citation("factR")
):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")

BiocManager::install("factR")
For older versions of R, please refer to the appropriate
Bioconductor release
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("factR")
factR
HTML
R Script
Reference Manual
PDF
NEWS
Text
LICENSE
Text
Need some help? Ask on the Bioconductor Support site!
Details
biocViews
AlternativeSplicing
FunctionalPrediction
GenePrediction
Software
Version
1.12.0
In Bioconductor since
BioC 3.16 (R-4.2) (3.5 years)
License
file
LICENSE
Depends
R (>= 4.2)
Imports
BiocGenerics
(>= 0.46),
Biostrings
(>= 2.68),
GenomeInfoDb
(>= 1.36),
dplyr
(>= 1.1),
GenomicFeatures
(>= 1.52),
GenomicRanges
(>= 1.52),
IRanges
(>= 2.34),
purrr
(>= 1.0),
rtracklayer
(>= 1.60),
tidyr
(>= 1.3), methods (>= 4.3),
BiocParallel
(>= 1.34),
S4Vectors
(>= 0.38),
data.table
(>= 1.14),
rlang
(>= 1.1),
tibble
(>= 3.2),
wiggleplotr
(>= 1.24),
RCurl
(>= 1.98),
XML
(>= 3.99),
drawProteins
(>= 1.20),
ggplot2
(>= 3.4),
stringr
(>= 1.5),
pbapply
(>= 1.7), stats (>= 4.3), utils (>= 4.3), graphics (>= 4.3),
crayon
(>= 1.5)
System Requirements
URL
See More
Suggests
AnnotationHub
(>= 2.22),
BSgenome
(>= 1.58),
BSgenome.Mmusculus.UCSC.mm10
testthat
knitr
rmarkdown
markdown
zeallot
rmdformats
bio3d
(>= 2.4),
signalHsmm
(>= 1.5),
tidyverse
(>= 1.3),
covr
patchwork
Linking To
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Imports Me
Suggests Me
Links To Me
Build Report
Build Report
Package Archives
Follow
Installation
instructions to use this package in your R session.
Source Package
factR_1.12.0.tar.gz
Windows Binary (x86_64)
factR_1.12.0.zip
macOS Binary (x86_64)
factR_1.12.0.tgz
macOS Binary (arm64)
factR_1.12.0.tgz
Source Repository
git clone https://git.bioconductor.org/packages/factR
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/factR
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